DanRer7 conservation lastz parameters

See Also:

• DanRer7 Genome size statistics
• DanRer7 conservation alignment
• Hg19 Genome size statistics
• Hg19 conservation alignment
• Hg19 Andy's alignment notes
• Hg18 44way blastz parameters
• Hg18 Genome size statistics
• Hg18 44way alignment

The default scoring matrix is:		The HoxD55 scoring matrix is:		The human-chimp.v2 scoring matrix is:
A C G T A 91 -114 -31 -123 C -114 100 -125 -31 G -31 -125 100 -114 T -123 -31 -114 91 O=400 E=30		A C G T A 91 -90 -25 -100 C -90 100 -100 -25 G -25 -100 100 -90 T -100 -25 -90 91 O=400 E=30		A C G T A 90 -330 -236 -356 C -330 100 -318 -236 G -236 -318 100 -330 T -356 -236 -330 90 O=600 E=150

do not edit, automatically generated table

query	abridged repeats(no)	M(40M)	K(3000)	L(3000)	Q	Y(9400)	program run	E(30)	H(0)	O(400)	T(1)	chain table date	% of danRer7 matched (chainLink table)	% of query matched (chainLinkCe9)
Stickleback gasAcu1	no	50	3000	3000	HoxD55.q	9400	lastz	30	0	400	1	2010-12-17	10.270%	N/A
Medaka oryLat2	no	50	3000	3000	HoxD55.q	9400	lastz	30	0	400	1	2010-12-17	10.032%	N/A
Tetraodon tetNig2	no	50	3000	3000	HoxD55.q	9400	lastz	30	0	400	1	2010-12-17	6.273%	N/A
Fugu fr2	no	50	3000	3000	HoxD55.q	9400	lastz	30	0	400	1	2010-12-21	7.363%	N/A
X. tropicalis xenTro2	no	40M	2200	6000	HoxD55.q	3400	lastz	30	2000	400	1	2010-12-17	6.428%	N/A
Mouse mm9	TBD
Human hg19	TBD